!sudo pip3 install https://elucidatainc.github.io/PublicAssets/builds/polly-python/tests/polly/polly_python-0.3.1_cohorts2-py3-none-any.whl
/bin/bash: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Collecting polly-python==0.3.1-cohorts2
Downloading https://elucidatainc.github.io/PublicAssets/builds/polly-python/tests/polly/polly_python-0.3.1_cohorts2-py3-none-any.whl (122 kB)
|████████████████████████████████| 122 kB 5.3 MB/s eta 0:00:01
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You should consider upgrading via the '/usr/local/bin/python3.10 -m pip install --upgrade pip' command.
from polly import analyze
AUTH_TOKEN=(os.environ['POLLY_REFRESH_TOKEN']) # Obtain authentication tokens
analysis = analyze.Analyze(AUTH_TOKEN)
analysis.identify_cohorts("bulkrnaseq_staging_oa","GSE193677_GPL16791_raw")
Factor Cohorts Number of Samples 0 demographics_gender Male 1314 1 demographics_gender Female 1174 2 ibd_clinicianmeasure_inactive_active Inactive 1526 3 ibd_clinicianmeasure_inactive_active Active 305 4 ibd_clinicianmeasure_inactive_active notgiven 657 5 diseasetypere UC.NonI 579 6 diseasetypere CD.NonI 737 7 diseasetypere UC.I 293 8 diseasetypere Control.NonI 460 9 diseasetypere CD.I 419 10 ibd_endoseverity_4levels Inactive 684 11 ibd_endoseverity_4levels Moderate 436 12 ibd_endoseverity_4levels notgiven 465 13 ibd_endoseverity_4levels Mild 713 14 ibd_endoseverity_4levels Severe 190 15 ibd_disease UC 843 16 ibd_disease CD 1152 17 ibd_disease Control 460 18 ibd_disease UC_Pouch 29 19 ibd_disease CD_Pouch 4 20 regionre Rectum 903 21 regionre Ileum 671 22 regionre Transverse 90 23 regionre Sigmoid 163 24 regionre Cecum 229 25 regionre LeftColon 180 26 regionre RightColon 252 27 study_eligibility_age_at_endo 40-60 945 28 study_eligibility_age_at_endo 20-40 1090 29 study_eligibility_age_at_endo 0-20 16 30 study_eligibility_age_at_endo NaN 0 31 study_eligibility_age_at_endo 60-80 393
| demographics_gender | ibd_clinicianmeasure_inactive_active | diseasetypere | ibd_endoseverity_4levels | ibd_disease | regionre | study_eligibility_age_at_endo | |
|---|---|---|---|---|---|---|---|
| geo_accession | |||||||
| GSM5976499 | Male | Inactive | UC.NonI | Inactive | UC | Rectum | 44 |
| GSM5976501 | Male | Inactive | UC.NonI | Inactive | UC | Ileum | 44 |
| GSM5976504 | Female | Active | CD.NonI | Inactive | CD | Transverse | 60 |
| GSM5976505 | Male | Inactive | CD.NonI | Moderate | CD | Sigmoid | 38 |
| GSM5976507 | Male | Active | UC.I | Moderate | UC | Rectum | 20 |
| ... | ... | ... | ... | ... | ... | ... | ... |
| GSM5978983 | Female | notgiven | Control.NonI | notgiven | Control | Cecum | 48 |
| GSM5978984 | Female | notgiven | Control.NonI | notgiven | Control | Rectum | 48 |
| GSM5978985 | Female | notgiven | Control.NonI | notgiven | Control | Rectum | 50 |
| GSM5978986 | Female | notgiven | Control.NonI | notgiven | Control | Cecum | 50 |
| GSM5978988 | Female | notgiven | Control.NonI | notgiven | Control | Rectum | 51 |
2488 rows × 7 columns
analysis.identify_cohorts("bulkrnaseq_staging_oa","GSE58135_GPL11154_raw")
Factor Cohorts \
0 source_name Breast Cancer Cell Line
1 source_name ER+ Breast Cancer Primary Tumor
2 source_name Triple Negative Breast Cancer Primary Tumor
3 source_name Uninvolved Breast Tissue Adjacent to ER+ Prima...
4 source_name Reduction Mammoplasty - No known cancer
5 source_name Uninvolved Breast Tissue Adjacent to TNBC Prim...
6 tissue Breast Cancer Cell Line
7 tissue ER+ Breast Cancer Primary Tumor
8 tissue Triple Negative Breast Cancer Primary Tumor
9 tissue Uninvolved Breast Tissue Adjacent to ER+ Prima...
10 tissue Reduction Mammoplasty - No known cancer
11 tissue Uninvolved Breast Tissue Adjacent to TNBC Prim...
Number of Samples
0 27
1 42
2 42
3 30
4 5
5 21
6 27
7 42
8 42
9 30
10 5
11 21
| source_name | tissue | |
|---|---|---|
| geo_accession | ||
| GSM1401648 | Breast Cancer Cell Line | Breast Cancer Cell Line |
| GSM1401651 | Breast Cancer Cell Line | Breast Cancer Cell Line |
| GSM1401659 | Breast Cancer Cell Line | Breast Cancer Cell Line |
| GSM1401660 | Breast Cancer Cell Line | Breast Cancer Cell Line |
| GSM1401661 | Breast Cancer Cell Line | Breast Cancer Cell Line |
| ... | ... | ... |
| GSM1401805 | Uninvolved Breast Tissue Adjacent to TNBC Prim... | Uninvolved Breast Tissue Adjacent to TNBC Prim... |
| GSM1401807 | Uninvolved Breast Tissue Adjacent to TNBC Prim... | Uninvolved Breast Tissue Adjacent to TNBC Prim... |
| GSM1401809 | Uninvolved Breast Tissue Adjacent to TNBC Prim... | Uninvolved Breast Tissue Adjacent to TNBC Prim... |
| GSM1401810 | Uninvolved Breast Tissue Adjacent to TNBC Prim... | Uninvolved Breast Tissue Adjacent to TNBC Prim... |
| GSM1401814 | Uninvolved Breast Tissue Adjacent to TNBC Prim... | Uninvolved Breast Tissue Adjacent to TNBC Prim... |
167 rows × 2 columns
analysis.identify_cohorts("bulkrnaseq_staging_oa","GSE95587_GPL16791_raw")
Factor Cohorts Number of Samples 0 gender sex: F 51 1 gender sex: M 65 2 disease diagnosis: Alzheimer's disease 83 3 disease diagnosis: control 33 4 braak_score V 21 .. ... ... ... 87 post_mortem_interval 3.27 1 88 post_mortem_interval 2.98 1 89 age_at_death NaN 0 90 age_at_death 0-20 2 91 age_at_death 40-60 1 [92 rows x 3 columns]
| gender | disease | braak_score | rin_score | age_at_death | post_mortem_interval | |
|---|---|---|---|---|---|---|
| geo_accession | ||||||
| GSM2516806 | sex: F | diagnosis: Alzheimer's disease | V | 6.9 | 97 | 3.16 |
| GSM2516809 | sex: M | diagnosis: control | III | 6.8 | 82 | 3.0 |
| GSM2516812 | sex: M | diagnosis: control | III | 5.1 | 73 | 2.0 |
| GSM2516815 | sex: M | diagnosis: Alzheimer's disease | IV | 6.1 | 78 | 3.33 |
| GSM2516821 | sex: M | diagnosis: control | IV | 8.2 | 82 | 3.0 |
| ... | ... | ... | ... | ... | ... | ... |
| GSM2516914 | sex: M | diagnosis: control | III | 6.0 | 97 | 1.87 |
| GSM2516915 | sex: F | diagnosis: Alzheimer's disease | IV | 6.3 | 82 | 4.5 |
| GSM2516916 | sex: F | diagnosis: Alzheimer's disease | IV | 7.3 | 93 | 2.15 |
| GSM2516918 | sex: M | diagnosis: control | III | 7.2 | 91 | 3.27 |
| GSM2516919 | sex: M | diagnosis: Alzheimer's disease | IV | 7.4 | 97 | 2.98 |
116 rows × 6 columns
analysis.identify_cohorts("bulkrnaseq_staging_oa","GSE143897_GPL16791_raw")
Factor Cohorts Number of Samples 0 source_name Serous Ovarian Cancer Tumor 75 1 source_name Benign_Tissue 11 2 source_name Ascites 28 3 tissue Serous Ovarian Cancer Tumor 75 4 tissue Benign_Tissue 11 .. ... ... ... 78 patientid 66 1 79 age NaN 0 80 age 40-60 25 81 age 60-80 20 82 age 20-40 2 [83 rows x 3 columns]
| source_name | tissue | stage | age | patientid | |
|---|---|---|---|---|---|
| geo_accession | |||||
| GSM4276367 | Serous Ovarian Cancer Tumor | Serous Ovarian Cancer Tumor | 4B | 61.0 | 1331-101 |
| GSM4276369 | Serous Ovarian Cancer Tumor | Serous Ovarian Cancer Tumor | 4 | 67.0 | 1331-103 |
| GSM4276370 | Serous Ovarian Cancer Tumor | Serous Ovarian Cancer Tumor | 4 | 67.0 | 1331-103 |
| GSM4276372 | Serous Ovarian Cancer Tumor | Serous Ovarian Cancer Tumor | 3C | 77.0 | 1331-3 |
| GSM4276374 | Serous Ovarian Cancer Tumor | Serous Ovarian Cancer Tumor | 3C | 74.0 | 1331-24 |
| ... | ... | ... | ... | ... | ... |
| GSM4276483 | Ascites | Ascites | 4 | 55.0 | 33 |
| GSM4276485 | Ascites | Ascites | 3C | 76.0 | 35 |
| GSM4276487 | Ascites | Ascites | 4 | 74.0 | 37 |
| GSM4276488 | Ascites | Ascites | 3C | 67.0 | 38 |
| GSM4276489 | Ascites | Ascites | 4 | 76.0 | 39 |
114 rows × 5 columns
analysis.identify_cohorts("bulkrnaseq_staging_oa","GSE171012_GPL20301_raw")
Factor Cohorts Number of Samples 0 tissue skin 50 1 tissue lesion 221 2 used_for_analysis TRUE 241 3 used_for_analysis FALSE 30 4 cell_type CD8 68 .. ... ... ... 246 sorted_cells 7826.0 1 247 sorted_cells 1159.0 1 248 sorted_cells 1273.0 1 249 sorted_cells 286.0 1 250 sorted_cells 856.0 1 [251 rows x 3 columns]
| tissue | used_for_analysis | cell_type | clinical_status | sequencing_lane | sequencing_batch | subject_id | sorted_cells | |
|---|---|---|---|---|---|---|---|---|
| geo_accession | ||||||||
| GSM5216064 | skin | TRUE | CD8 | Healthy | L008 | n050317 | N11 | 7867.0 |
| GSM5216066 | skin | TRUE | Treg | Healthy | L008 | n050317 | N11 | 259.0 |
| GSM5216072 | skin | TRUE | CD8 | Healthy | L001 | n040618 | N17 | 114547.0 |
| GSM5216074 | skin | TRUE | Treg | Healthy | L001 | n040618 | N17 | 16542.0 |
| GSM5216076 | skin | TRUE | Teff | Healthy | L005 | n011118 | N18 | 33387.0 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... |
| GSM5216320 | lesion | TRUE | Teff | Psoriasis_PreTreatment | L004 | n062518 | PSO38 | 1273.0 |
| GSM5216325 | lesion | TRUE | CD8 | Psoriasis_SecukinumabTreatmentWeek2 | L004 | n062518 | PSO38 | 286.0 |
| GSM5216327 | lesion | TRUE | Treg | Psoriasis_SecukinumabTreatmentWeek12 | L005 | n062518 | PSO38 | 856.0 |
| GSM5216330 | lesion | TRUE | bulk | Psoriasis_SecukinumabTreatmentWeek12 | L005 | n062518 | PSO38 | notgiven |
| GSM5216334 | lesion | TRUE | bulk | Psoriasis_SecukinumabTreatmentWeek4 | L005 | n062518 | PSO38 | notgiven |
271 rows × 8 columns
# About 2k samples with timestamp
analysis.identify_cohorts('bulkrnaseq_staging_oa', 'GSE47774_GPL11154_raw')
Factor Cohorts \
0 extract_protocol Illumina, SOLiD, and 454 libraries were prepar...
1 extract_protocol libraries were prepared using standard Illumin...
2 submission_date 2013:06:10
3 submission_date 2014:04:02
4 data_processing Illumina Casava1.8 software used for Illumina ...
.. ... ...
69 barcode ATTCCT
70 barcode GTCCGC
71 barcode GTGGCC
72 barcode GTGAAA
73 barcode GTTTCG
Number of Samples
0 1579
1 140
2 1579
3 140
4 1579
.. ...
69 47
70 7
71 7
72 7
73 7
[74 rows x 3 columns]
| extract_protocol | submission_date | data_processing | library_id | source_name | seqc_sample | site | lane | flowcell | barcode | |
|---|---|---|---|---|---|---|---|---|---|---|
| geo_accession | ||||||||||
| GSM1156798 | Illumina, SOLiD, and 454 libraries were prepar... | 2013:06:10 | Illumina Casava1.8 software used for Illumina ... | 1 | Universal Human Reference RNA (UHRR) from Stra... | A | BGI | L01 | BC0AYPACXX | ATCACG |
| GSM1156799 | Illumina, SOLiD, and 454 libraries were prepar... | 2013:06:10 | Illumina Casava1.8 software used for Illumina ... | 1 | Universal Human Reference RNA (UHRR) from Stra... | A | BGI | L02 | AC0AYTACXX | ATCACG |
| GSM1156801 | Illumina, SOLiD, and 454 libraries were prepar... | 2013:06:10 | Illumina Casava1.8 software used for Illumina ... | 1 | Universal Human Reference RNA (UHRR) from Stra... | A | BGI | L03 | AC0AYTACXX | ATCACG |
| GSM1156802 | Illumina, SOLiD, and 454 libraries were prepar... | 2013:06:10 | Illumina Casava1.8 software used for Illumina ... | 1 | Universal Human Reference RNA (UHRR) from Stra... | A | BGI | L03 | BC0AYPACXX | ATCACG |
| GSM1156803 | Illumina, SOLiD, and 454 libraries were prepar... | 2013:06:10 | Illumina Casava1.8 software used for Illumina ... | 1 | Universal Human Reference RNA (UHRR) from Stra... | A | BGI | L04 | AC0AYTACXX | ATCACG |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| GSM1362103 | libraries were prepared using standard Illumin... | 2014:04:02 | Illumina Casava1.8 software used for Illumina ... | 1 | Mix of A and B (1:3) | F | NYG | L05 | AC132FACXX | GTGAAA |
| GSM1362106 | libraries were prepared using standard Illumin... | 2014:04:02 | Illumina Casava1.8 software used for Illumina ... | 1 | Mix of A and B (1:3) | F | NYG | L08 | AC132FACXX | GTGAAA |
| GSM1362107 | libraries were prepared using standard Illumin... | 2014:04:02 | Illumina Casava1.8 software used for Illumina ... | 2 | Mix of A and B (1:3) | F | NYG | L02 | AC132FACXX | GTTTCG |
| GSM1362109 | libraries were prepared using standard Illumin... | 2014:04:02 | Illumina Casava1.8 software used for Illumina ... | 2 | Mix of A and B (1:3) | F | NYG | L04 | AC132FACXX | GTTTCG |
| GSM1362113 | libraries were prepared using standard Illumin... | 2014:04:02 | Illumina Casava1.8 software used for Illumina ... | 2 | Mix of A and B (1:3) | F | NYG | L08 | AC132FACXX | GTTTCG |
1719 rows × 10 columns